Digital Commons Network^™

Machine Learning Approaches For Phenotype Refinement To Improve Genetic Association Analysis, Jiangwen Sun

Doctoral Dissertations

Unlike univariate phenotypes such as human height, multivariate phenotypes such as substance use disorders, are characterized by multiple low level phenotypic features. Due to the substantial variation in the multivariate features, these phenotypes are heterogeneous. This phenotypic heterogeneity substantially limits the success in uncovering genetic factors of the phenotype. The identification of homogeneous disease subtypes can be both necessary and beneficial. Despite great progress in molecular genetics that allows the genomewide identification of common and rare variants, there is considerably less progress in the refinement of phenotypes.

The most recent and sophisticated phenotype refinement approaches perform unsupervised cluster analysis to …

Novel Human Embryonic Stem Cell Regulators Identified By Conserved And Distinct Cpg Island Methylation State, Steve Pells, Eirini Koutsouraki, Sofia Morfopoulou, Sara Valencia-Cadavid, Simon R. Tomlinson, Ravi Kalathur, Matthias E. Futschik, Sousa Pa De

School of Biomedical Sciences

No abstract provided.

The Kynurenine Pathway Of Tryptophan Catabolism And Aids-Associated Kaposi's Sarcoma In Africa, Helen Byakwaga, Peter W. Hunt, Miriam Laker-Oketta, David V. Glidden, Yong Huang, Bosco M. Bwana, Rain Mocello, John Bennett, Victoria Walusansa, Sheila C. Dollard, David R. Bangsberg, Edward K. Mbidde, Jeffrey N. Martin

OHSU-PSU School of Public Health Faculty Publications and Presentations

Background—Other than Kaposi's sarcoma (KS)-associated herpesvirus and CD4+ T cell lymphopenia, the mechanisms responsible for KS in the context of HIV are poorly understood. One recently explored pathway of HIV pathogenesis involves induction of the enzyme indoleamine 2,3 dioxygenase-1 (IDO), which catabolizes tryptophan into kynurenine and several other immunologically active metabolites that suppress T cell proliferation. We investigated the role of IDO in the development of KS in HIV disease.

Methods—In a case-control study among untreated HIV-infected Ugandans, cases were adults with KS and controls were without KS. IDO activity was assessed by the ratio of plasma kynurenine to tryptophan …

A Self-Lysis Pathway That Enhances The Virulence Of A Pathogenic Bacterium, Kirsty A. Mcfarland, Emily L. Dolben, Michele Leroux, Tracy K. Kambara, Kathryn Ramsey, Robin Kirkpatrick, Joseph Mougous, Deborah Hogan, Simon Dove

Dartmouth Scholarship

In mammalian cells, programmed cell death (PCD) plays important roles in development, in the removal of damaged cells, and in fighting bacterial infections. Although widespread among multicellular organisms, there are relatively few documented instances of PCD in bacteria. Here we describe a potential PCD pathway in Pseudomonas aeruginosa that enhances the ability of the bacterium to cause disease in a lung infection model. Activation of the system can occur in a subset of cells in response to DNA damage through cleavage of an essential transcription regulator we call AlpR. Cleavage of AlpR triggers a cell lysis program through de-repression of …

New Data On The Early - Middle Badenian Transition In The Nw Transylvanian Basin (Romania) Revealed By The Planktonic Foraminifera Assemblages, Rodica Filipescu, Sorin Filipescu

Studia UBB Geologia

The planktonic foraminifera assemblages recovered from two cores drilled in Cluj-Napoca (NW Transylvanian Basin) demonstrate connections of the basin to the open seas before the middle Badenian evaporite deposition. Assemblages suggest clear changes in the environments, with an initial transgressive trend, followed by a decrease in the rate of sea-level rise, and finally a sea-level fall. The occurrence of planktonic foraminifera (mainly Globorotalia) offers a good potential for correlation of the pre-evaporitic interval with the uppermost Langhian and can be used for tracing the early-middle Badenian boundary.

Hect E3 Ubiquitin Ligase Itch Functions As A Novel Nega, Gary T. Zeruth, Jason G. Williams, Yasemin C. Cole, Anton M. Jetten

Faculty & Staff Research and Creative Activity

The transcription factor Gli-similar 3 (Glis3) plays a critical role in the generation of pancreatic ß cells and the regulation insulin gene transcription and has been implicated in the development of several pathologies, including type 1 and 2 diabetes and polycystic kidney disease. However, little is known about the proteins and posttranslational modifications that regulate or mediate Glis3 transcriptional activity. In this study, we identify by mass-spectrometry and yeast 2-hybrid analyses several proteins that interact with the N-terminal region of Glis3. These include the WW-domain-containing HECT E3 ubiquitin ligases, Itch, Smurf2, and Nedd4. The interaction between Glis3 and the HECT …

The Social Environmental Elements Of Resilience Among Vulnerable African American/Black Men Who Have Sex With Men, Mance E. Buttram

CAHSS Faculty Articles

Resilience theory has been suggested as a strong framework for research on HIV prevention among men who have sex with men (MSM). Among this population, literature indicates that African American/Black MSM are particularly vulnerable to health and social disparities associated with HIV transmission risk. Conceptualizing resilience as a part of one’s social environment, this qualitative study investigates the specific elements of resilience, and the associated contexts and relationships, among a sample of 21 substance-using African American/Black MSM. Data indicate that (1) elements contributing to resilience are multiple and co-occurring, including inner strengths, social relationships, diversity of experience, religion/spirituality, altruism, and …

The Interaction Between Fluid Wall Shear Stress And Solid Circumferential Strain Affects Endothelial Gene Expression, Ronny Amaya, Alexis Pierides, John M. Tarbell

Publications and Research

Endothelial cells lining the walls of blood vessels are exposed simultaneously to wall shear stress (WSS) and circumferential stress (CS) that can be characterized by the temporal phase angle between WSS and CS (stress phase angle – SPA). Regions of the circulation with highly asynchronous hemodynamics (SPA close to -180°) such as coronary arteries are associated with the development of pathological conditions such as atherosclerosis and intimal hyperplasia whereas more synchronous regions (SPA closer to 0°) are spared of disease. The present study evaluates endothelial cell gene expression of 42 atherosclerosis-related genes under asynchronous hemodynamics (SPA=-180 °) and synchronous hemodynamics …

American Farm Bureau Federatio V. Epa

2015 Decisions

USDC for the Middle District of Pennsylvania

Century-Long Warming Trends In The Upper Water Column Of Lake Tanganyika, Benjamin Kraemer, Simon Hook, Timo Huttula, Pekka Kotilainen, Catherine M. O'Reilly, Anu Peltonen, Pierre-Denis Plisnier, Jouko Sarvala, Rashid Tamatamah, Yvonne Vadeboncoeur, Bernhard Wehrli, Peter B. Mcintyre

Biological Sciences Faculty Publications

Lake Tanganyika, the deepest and most voluminous lake in Africa, has warmed over the last century in response to climate change. Separate analyses of surface warming rates estimated from in situ instruments, satellites, and a paleolimnological temperature proxy (TEX86) disagree, leaving uncertainty about the thermal sensitivity of Lake Tanganyika to climate change. Here, we use a comprehensive database of in situ temperature data from the top 100 meters of the water column that span the lake’s seasonal range and lateral extent to demonstrate that long-term temperature trends in Lake Tanganyika depend strongly on depth, season, and latitude. The observed spatiotemporal …

Cyclometalated Iminophosphorane Gold(Iii) And Platinum(Ii) Complexes. A Highly Permeable Cationic Platinum(Ii) Compound With Promising Anticancer Properties, Malgorzata Frik, Jacob Fernández-Gallardo, Oscar Gonzalo, Víctor Mangas-Sanjuan, Marta González-Alvarez, Alfonso Serrano Del Valle, Chunhua Hu, Isabel González-Alvarez, Marival Bermejo, Isabel Marzo, María Contel

Publications and Research

New organometallic gold(III) and platinum(II) complexes containing iminophosphorane ligands are described. Most of them are more cytotoxic to a number of human cancer cell lines than cisplatin. Cationic Pt(II) derivatives 4 and 5, which differ only in the anion, Hg2Cl62– or PF6– respectively, display almost identical IC50 values in the sub-micromolar range (25–335-fold more active than cisplatin on these cell lines). The gold compounds induced mainly caspase-independent cell death, as previously reported for related cycloaurated compounds containing IM ligands. Cycloplatinated compounds 3, 4, and 5 can also activate alternative caspase-independent mechanisms of death. However, at short incubation times cell death …

Selective Impact Of Disease On Coral Communities: Outbreak Of White Syndrome Causes Significant Total Mortality Of Acropora Plate Corals, Jean-Paul A. Hobbs, Ashley J. Frisch, Stephen J. Newman, Corey B. Wakefield

Fisheries Research Articles

Coral diseases represent a significant and increasing threat to coral reefs. Among the most destructive diseases is White Syndrome (WS), which is increasing in distribution and prevalence throughout the Indo-Pacific. The aim of this study was to determine taxonomic and spatial patterns in mortality rates of corals following the 2008 outbreak of WS at Christmas Island in the eastern Indian Ocean. WS mainly affected Acropora plate corals and caused total mortality of 36% of colonies across all surveyed sites and depths. Total mortality varied between sites but was generally much greater in the shallows (0–96% of colonies at 5 m …

Development And Study Of Waterproof Breathable Fabric Using Silicone Oil And Polyurethane Binder, Aditi S. Bakshi

Master's Theses and Doctoral Dissertations

The focus of this study is on determining the optimum combination of hydrophilic and hydrophobic components in coating material to obtain high breathability and waterproof properties. Polyurethane binder and silicone oil were used in eight different combinations to coat the fabric along with one sample with 100% polyurethane binder for control. A knife-over-roll coating machine was used to coat the fabric. The coated samples were tested by using the Sweating Guarded Hot Plate method for breathability and the spray test and contact angle method for waterproof properties. Results obtained from the tests showed that fabric coated with an 80%-20% and …

Hybridization Of Indigenous Knowledge And Documentation Of Intangible Cultural Heritage Of Batticaloa District Of Sri Lanka, Thankavadivel Ramanan

Proceedings of the IATUL Conferences

No abstract provided.

Strategic Partnerships For New Perspectives On Teaching Information Literacy To Students Of Industrial Engineering And Management, Simone Kibler

Proceedings of the IATUL Conferences

No abstract provided.

Innovative Usage Of Unstructured Information Sources: From Text- And Data-Mining To Model-Driven Decision-Support, Martin Hofmann-Apitius

Proceedings of the IATUL Conferences

No abstract provided.

Applications Of Bregman Divergence Measures In Bayesian Modeling, Gyuhyeong Goh

Doctoral Dissertations

This dissertation has mainly focused on the development of statistical theory, methodology, and application from a Bayesian perspective using a general class of divergence measures (or loss functions), called Bregman divergence. Many applications of Bregman divergence have played a key role in recent advances in machine learning. My goal is to turn the spotlight on Bregman divergence and its applications in Bayesian modeling. Since Bregman divergence includes many well-known loss functions such as squared error loss, Kullback-Leibler divergence, Itakura-Saito distance, and Mahalanobis distance, the theoretical and methodological development unify and extend many existing Bayesian methods. The broad applicability of both …

Testing And Evaluating Dye Color: A Study Using Spectrophotometry On Technicolor And Eastman Color Motion Picture Film, Melissa Sagen

Theses

The history of color motion picture film is linked to two companies: Technicolor and Eastman Kodak. Technicolor was formed in 1915 by Herbert Kalmus, Daniel Comstock, and W. Burton Wescott, who realized that color film could enhance motion picture entertainment. Introduced in 1932, it was a three-color process that was widely used into the late 1950s. The three-color process utilized a camera with one lens that exposed three black and white negatives simultaneously by splitting the incoming visible light through a prism. The prism would create two beams of light which would then expose one film negative to green light …

Multinational Perspectives On Information Technology From Academia And Industry, Mihaela C. Sabin, John Impagliazzo, Hala Alrumaih, Brenda Byers, Daina Gudoniene, Margaret Hamilton, Vsevolod Kotlyarov, Barry Lunt, James W. Mcguffee, Svetlana Peltsverger, Cara Tang, Barbara Viola, Ming Zhang

Applied Engineering and Sciences Scholarship

As the term 'information technology' has many meanings for various stakeholders and continues to evolve, this work presents a comprehensive approach for developing curriculum guidelines for rigorous, high quality, bachelor's degree programs in information technology (IT) to prepare successful graduates for a future global technological society. The aim is to address three research questions in the context of IT concerning (1) the educational frameworks relevant for academics and students of IT, (2) the pathways into IT programs, and (3) graduates' preparation for meeting future technologies. The analysis of current trends comes from survey data of IT faculty members and professional …

Genomic Copy Number Variation In Mus Musculus., M Elizabeth O Locke, Maja Milojevic, Susan T Eitutis, Nisha Patel, Andrea E Wishart, Mark Daley, Kathleen A. Hill

Brain and Mind Institute Researchers' Publications

BACKGROUND: Copy number variation is an important dimension of genetic diversity and has implications in development and disease. As an important model organism, the mouse is a prime candidate for copy number variant (CNV) characterization, but this has yet to be completed for a large sample size. Here we report CNV analysis of publicly available, high-density microarray data files for 351 mouse tail samples, including 290 mice that had not been characterized for CNVs previously.

RESULTS: We found 9634 putative autosomal CNVs across the samples affecting 6.87% of the mouse reference genome. We find significant differences in the degree of …

Mechanotransduction: Use The Force(S), Ewa K. Paluch, Celeste M. Nelson, Nicolas Biais, Ben Fabry, Jens Moeller, Beth L. Pruitt, Carina Wollnik, Galina Kudryasheva, Florian Rehfeldt, Walter Federle

Publications and Research

Mechanotransduction - how cells sense physical forces and translate them into biochemical and biological responses - is a vibrant and rapidly-progressing field, and is important for a broad range of biological phenomena. This forum explores the role of mechanotransduction in a variety of cellular activities and highlights intriguing questions that deserve further attention.

Organizations Don’T Resist Change, People Do: Modeling Individual Reactions To Organizational Change Through Loss And Terror Management, James R. Bailey, Jonathan D. Raelin

Organization Management Journal

This article has three premises that stand in contrast to emphases found in contemporary organizational change research. First, examination of resistance must start with the individual. Organizations don’t resist change, people do. Second, people react not to the change per se, but to the loss it represents. Third, loss engenders a deeply rooted peril response that is largely emotional in nature. To support these premises, we apply Terror Management Theory to locate resistance in existential buffers: emotional defense mechanisms that prevent awareness of loss and allow participation in a larger meaningful system. We argue that the buffers threatened during organizational …

The Impact Of External Contexts On Alliance Governance In Biotech–Pharmaceutical Firm Alliances, Joanne L. Scillitoe, Shanthi Gopalakrishnan, Michael D. Santaro

Organization Management Journal

The interest in strategic alliances has increased over the years, especially in high tech global industries such as biotechnology, as firms seek to gain access to needed resources, expertise, and knowledge for developing and commercializing new products and technologies. The governance structure of these alliances, which is an important consideration in understanding alliance formation and performance, is influenced by both external and internal contexts of the alliance partners. However, evidence from prior research has been inconclusive regarding the impact of external contexts on alliance governance selection. To better understand this impact, we simultaneously examine three key partner external contexts - …

Scuttling Iuu Fishing And Rewarding Sustainable Fishing: Enhancing The Effectiveness Of The Port State Measures Agreement With Trade-Related Measures, Anastasia Telesetsky

Seattle University Law Review

Illegal, unreported, and unregulated fishing (IUU fishing) is a substantial threat to global food security and a recurring problem for global fishery managers already facing difficult baseline situations exacerbated by climate change, including warming oceans and increasing acidification. There is nothing historically new about IUU fishing; there have always been poachers who take advantage of operating in the shadows of legal commercial fishing. What is new is the extent to which marine poaching has industrialized. It is estimated that 19% of the worldwide value of marine catches are unlawful. The problem is not limited to developing states. For example, even …

Ag Gag Past, Present, And Future, Justin F. Marceau

Seattle University Law Review

While the animal rights and food justice movements are relatively young, their political unpopularity has generated a steady onslaught of legislation designed to curtail their effectiveness. At each stage of their nascent development, these movements have confronted a new wave of criminal or civil sanctions carefully tailored to combat the previous successes the movements had achieved.

Intestacy Concerns For Same-Sex Couples: How Variations In State Law And Policy Affect Testamentary Wishes, Megan Moser

Seattle University Law Review

As the number of same-sex couples increases in the United States, concerns regarding the evolution of federal and state law, with respect to rights for same-sex couples, also continue to rise. As marriage is not always available to same-sex couples, they often face very different legal issues than couples in a traditional marriage. Because marriage is typically not a legal cause of action, the question of a marriage’s validity often arises incidentally to another legal question, such as the disposition of a decedent’s estate.

The Role Of The Pericardium In The Valveless, Tubular Heart Of The Tunicate, Ciona Savignyi, Lindsay D. Waldrop, Laura A. Miller

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Tunicates, small invertebrates within the phylum Chordata, possess a robust tubular heart which pumps blood through their open circulatory systems without the use of valves. This heart consists of two major components: the tubular myocardium, a flexible layer of myocardial cells that actively contracts to drive fluid down the length of the tube; and the pericardium, a stiff, outer layer of cells that surrounds the myocardium and creates a fluid-filled space between the myocardium and the pericardium. We investigated the role of the pericardium through in vivo manipulations on tunicate hearts and computational simulations of the myocardium and pericardium using …

Re-Tooling Marine Food Supply Resilience In A Climate Change Era: Some Needed Reforms, Robin Kundis Craig

Seattle University Law Review

Ocean fisheries and marine aquaculture are an important but often overlooked component of world food security. For example, of the seven billion (and counting) people on the planet, over one billion depend on fish as their primary source of protein, and fish is a primary source of protein (30 percent or more of protein consumed) in many countries around the world, including Japan, Greenland, Taiwan, Indonesia, several countries in Africa, and several South Pacific island nations. Marine fisheries and marine aquaculture have been subject to a number of stressors that can undermine world food security, including overfishing, habitat destruction, and …

Increased Resting-State Functional Connectivity Of Visual- And Cognitive-Control Brain Networks After Training In Children With Reading Difficulties, Tzipi Horowitz-Kraus, Mark Difrancesco, Benjamin Kay, Yingying Wang, Scott K. Holland

Center for Brain, Biology, and Behavior: Faculty Publications

The Reading Acceleration Program, a computerized reading-training program, increases activation in neural circuits related to reading.We examined the effect of the training on the functional connectivity between independent components related to visual processing, executive functions, attention, memory, and language during rest after the training. Children 8–12 years old with reading difficulties and typical readers participated in the study. Behavioral testing and functional magnetic resonance imaging were performed before and after the training. Imaging data were analyzed using an independent component analysis approach. After training, both reading groups showed increased single-word contextual reading and reading comprehension scores. Greater positive correlations between …

Ceramides Promote Apoptosis For Virus-Infected Lymphoma Cells Through Induction Of Ceramide Synthases And Viral Lytic Gene Expression, Lu Dai, Jimena Trillo-Tinoco, Aiping Bai, Yihan Chen, Jacek Bielawski, Luis Del Valle, Charles D. Smith, Augusto C. Ochoa, Zhiqiang Qin, Chris Parsons

School of Medicine Faculty Publications

Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent for several human cancers including primary effusion lymphoma (PEL), a rapidly progressive malignancy arising preferentially in immunocompromised patients. With conventional chemotherapy, PEL continues to portend high mortality, dictating the development of novel therapeutic strategies. Sphingosine kinase 2 (SphK2) represents a key gatekeeper for sphingolipid metabolism, responsible for conversion of ceramides to sphingosine-1-phosphate (S1P). We have previously demonstrated that targeting SphK2 using a novel selective inhibitor, ABC294640, leads to intracellular accumulation of ceramides and induces apoptosis for KSHV-infected PEL cells, while suppressing tumor progression in vivo. In the current study, we sought to …